I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after
In terminal (ASSUMING shell is bash), a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5 b) export SUBJECTS_DIR=`pwd` c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot
Reuben A.
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Hi Reuben,
What template are you trying to use?
Regards, Thomas
On Tue, Aug 9, 2022 at 8:39 PM Addison, Reuben RAddison@mghihp.edu wrote:
I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after
In terminal (ASSUMING shell is bash),
a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5
b) export SUBJECTS_DIR=`pwd`
c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot
Reuben A. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/14BSO78GWppkTSRxKy0_i21J54-E8l5zZEm_fmrcGsTk5kd... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1xSShaGz-dpcP-PLGR28kIpu-3fSoQL4tbE_iu8A44CCg4N... < https://secure-web.cisco.com/1xSShaGz-dpcP-PLGR28kIpu-3fSoQL4tbE_iu8A44CCg4N... . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
The Yeo et al, 2011 template
Reuben A.
Get Outlook for iOShttps://aka.ms/o0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Thomas Yeo ythomas@csail.mit.edu Sent: Sunday, August 14, 2022 6:59:51 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Parcellation issue
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Hi Reuben,
What template are you trying to use?
Regards, Thomas
On Tue, Aug 9, 2022 at 8:39 PM Addison, Reuben <RAddison@mghihp.edumailto:RAddison@mghihp.edu> wrote:
I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after
In terminal (ASSUMING shell is bash),
a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5
b) export SUBJECTS_DIR=`pwd`
c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot
Reuben A.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/14BSO78GWppkTSRxKy0_i21J54-E8l5zZEm_fmrcGsTk5kdPqWEMlcdurhaFzwcXEUJxf_Ua-Mb4G-EjPqolSOyfPp3L-2iazGuf1ZiXH7PrunKUL-vDO0vylguwgxRcHhyn_LMatCC5B5i7b0BT99mTDw8bJLNpC4luB-CHTRDezMvrGno9aLbajAfIA7RpfOQEes3940XLdioVzOBgkcjXmsNaRPVzeY8vG0UQGOZ_wtDPnBYwtWhyXmKPu8vJWJYfrrdieXNDa6bjpaBQCtTuM94YwvtpQfzKJl7o4zr7N9qOgvS7OmGriFKlOEmmMYH7Xc-_QLkOWO8O0VwkL5g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1xSShaGz-dpcP-PLGR28kIpu-3fSoQL4tbE_iu8A44CCg4NaYMVbQs-xmQnbwekrjTSL_HCgfxKztCKV1NxXGvj7E6uxBq5U700tWPWjSkJbPYPaPxBkHGYem5RV500zrfrFO6TxoHXTz3F7jmcvIXjlrWqDbl29UDs8QrIEReEJ52Fo2K1JI7hlYPMywQsq-vg3-80k3H75KSFM-VxaYEeKCvGeElxlzzYXC2xEtuHhCS1TtpqrbKynoq1CAMEaOcpdzaZLZ4bpaIvMHofYJqY3c8m9px1mAnfzEg2hIRgYPIgPo0qmnv7kf88wWUyI3t1XqSAOMapEgW0hL4oim0A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/compliancelinehttps://secure-web.cisco.com/1xSShaGz-dpcP-PLGR28kIpu-3fSoQL4tbE_iu8A44CCg4NaYMVbQs-xmQnbwekrjTSL_HCgfxKztCKV1NxXGvj7E6uxBq5U700tWPWjSkJbPYPaPxBkHGYem5RV500zrfrFO6TxoHXTz3F7jmcvIXjlrWqDbl29UDs8QrIEReEJ52Fo2K1JI7hlYPMywQsq-vg3-80k3H75KSFM-VxaYEeKCvGeElxlzzYXC2xEtuHhCS1TtpqrbKynoq1CAMEaOcpdzaZLZ4bpaIvMHofYJqY3c8m9px1mAnfzEg2hIRgYPIgPo0qmnv7kf88wWUyI3t1XqSAOMapEgW0hL4oim0A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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Hi Rueben,
I am afraid I don't understand your question. The Yeo networks are available in fsaverage and FSL MNI152 space.
If your data is already in fsaverage or FSL MNI152 space, you can simply use the networks directly without running recon-all.
Can you elaborate more on what you are trying to do?
Regards, Thomas
On Mon, Aug 15, 2022 at 7:20 AM Addison, Reuben RAddison@mghihp.edu wrote:
The Yeo et al, 2011 template
Reuben A.
Get Outlook for iOS https://secure-web.cisco.com/15lbsHnRV10gWZWym8hAq7jnJ3r-m7bvLeyJenniJmGOpMIsZEHKqBDJ2eF3NGSXqUdErU2WDGT2YW_lu4PS3Vof6Y948sJa49P63oeRql5Dma74Aum1LPqGWiqw9svLE3I-vbYDObRpvWjqMNibRyQRE_AxMxWkqa4Q0FtTE4R-x-ITxj5eg61OpzU--92q-aYXm3PZkrs9uUctKbwftQOE4PxNQ98bmm21Fm8nkOyNYJ9MO38zazIm4tNy-J2GigE0M_SzRmvBMmPQoTMz86mEnqv2TqH8UGPMG_MYSS6eyUvqOhocj7cb9agzXFqxGlXS25y0e2fUg2jCdk5LTdQ/https%3A%2F%2Faka.ms%2Fo0ukef
*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Thomas Yeo < ythomas@csail.mit.edu> *Sent:* Sunday, August 14, 2022 6:59:51 PM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Parcellation issue
External Email - Use CautionHi Reuben,
What template are you trying to use?
Regards, Thomas
On Tue, Aug 9, 2022 at 8:39 PM Addison, Reuben RAddison@mghihp.edu wrote:
I want to use a different template apart from the MNI for my parcellation (Yeo_JNeurophysiol11_FreeSurfer.zip). Below are the instructions given in the readme. My question is – do I need to run this code before Recon-all or after
In terminal (ASSUMING shell is bash),
a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5
b) export SUBJECTS_DIR=`pwd`
c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot
Reuben A. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1uJka6ZxGDk9uv1UdxIdtxFdOFoN25i0y-CBAB1SUkI7xUK... https://secure-web.cisco.com/14BSO78GWppkTSRxKy0_i21J54-E8l5zZEm_fmrcGsTk5kdPqWEMlcdurhaFzwcXEUJxf_Ua-Mb4G-EjPqolSOyfPp3L-2iazGuf1ZiXH7PrunKUL-vDO0vylguwgxRcHhyn_LMatCC5B5i7b0BT99mTDw8bJLNpC4luB-CHTRDezMvrGno9aLbajAfIA7RpfOQEes3940XLdioVzOBgkcjXmsNaRPVzeY8vG0UQGOZ_wtDPnBYwtWhyXmKPu8vJWJYfrrdieXNDa6bjpaBQCtTuM94YwvtpQfzKJl7o4zr7N9qOgvS7OmGriFKlOEmmMYH7Xc-_QLkOWO8O0VwkL5g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1hNznAV9hii2pdFzVk5GKoQ2jgbVqROxuu4CrgCUQmZYEk7... https://secure-web.cisco.com/1xSShaGz-dpcP-PLGR28kIpu-3fSoQL4tbE_iu8A44CCg4NaYMVbQs-xmQnbwekrjTSL_HCgfxKztCKV1NxXGvj7E6uxBq5U700tWPWjSkJbPYPaPxBkHGYem5RV500zrfrFO6TxoHXTz3F7jmcvIXjlrWqDbl29UDs8QrIEReEJ52Fo2K1JI7hlYPMywQsq-vg3-80k3H75KSFM-VxaYEeKCvGeElxlzzYXC2xEtuHhCS1TtpqrbKynoq1CAMEaOcpdzaZLZ4bpaIvMHofYJqY3c8m9px1mAnfzEg2hIRgYPIgPo0qmnv7kf88wWUyI3t1XqSAOMapEgW0hL4oim0A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1hNznAV9hii2pdFzVk5GKoQ2jgbVqROxuu4CrgCUQmZYEk7... https://secure-web.cisco.com/1xSShaGz-dpcP-PLGR28kIpu-3fSoQL4tbE_iu8A44CCg4NaYMVbQs-xmQnbwekrjTSL_HCgfxKztCKV1NxXGvj7E6uxBq5U700tWPWjSkJbPYPaPxBkHGYem5RV500zrfrFO6TxoHXTz3F7jmcvIXjlrWqDbl29UDs8QrIEReEJ52Fo2K1JI7hlYPMywQsq-vg3-80k3H75KSFM-VxaYEeKCvGeElxlzzYXC2xEtuHhCS1TtpqrbKynoq1CAMEaOcpdzaZLZ4bpaIvMHofYJqY3c8m9px1mAnfzEg2hIRgYPIgPo0qmnv7kf88wWUyI3t1XqSAOMapEgW0hL4oim0A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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freesurfer@nmr.mgh.harvard.edu
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Addison, Reuben -
Thomas Yeo